natverse.github.io

This repo is the source of https://natverse.github.io/, and this readme tells you how it all works.

• If you spot any small problems with the website, please feel empowered to fix them directly with a PR generated by editing any of the markdown files at https://github.com/natverse/natverse_hugo.

• If you see any larger problems, an issue is probably better: that way we can discuss the problem before you commit any time to it.

• If you'd like to contribute a blog post, please chat with one of us first. Then read the contributing guide.

This repo (and resulting website) is licensed as CC BY-SA.

Recommended setup for editing the website

If you want to make regular edits to the website then one easy way to do this is using Rstudio and the blogdown package. First install Rstudio/R as normal.

Install blogdown/hugo (once only steps)

install.packages("blogdown")
# nb this can take some time to complete
blogdown::install_hugo()

Git clone the repository

Use git to clone the repository.

# or wherever you would like to clone to
cd ~/dev_pages/
git clone git@github.com:natverse/natverse_hugo.git

Please make sure you have checked out the dev_pages branch (this is actually the default).

Serve the site locally

This site/theme expects an older Hugo release (0.54.x). If you have a newer Hugo installed globally, set a project-specific Hugo version in R:

blogdown::install_hugo(version = "0.54.0", os = "macOS", arch = "64bit", extended = TRUE)
options(blogdown.hugo.version = "0.54.0")

Then serve as usual:

blogdown::serve_site()

You can now edit your markdown files in /content/ and each time you save the live local preview of the site will be updated.

Saving your changes

• Check out the git dev_pages branch
• Commit each distinct change in git
• Make sure that the site works OK locally (with blogdown::serve_site())

Update the public site

When you are ready, push your changes (in the dev_pages branch) to the remote GitHub repository and the site will automatically be rebuilt (via the netlify integration). You should ensure that the dev_pages branch has successfully rebuilt. If and only if this has happened, you can merge the dev_pages branch into the master branch, which will then trigger a rebuild of the public facing website.

Manual GitHub Pages deploy

If CI deploy is unavailable, publish manually to natverse/natverse.github.io:

# from natverse_hugo
./scripts/deploy_github_pages.sh ../natverse.github.io

# then commit + push in the target repo
cd ../natverse.github.io
git add -A
git commit -m "Update site"
git push origin master

For publication count updates, re-render before deploying:

Rscript scripts/update_publications.R

Acknowledgements

We are extremely grateful to the authors of the following:

• Hugo
• blogdown
• tidyverse.org
• tourmaline hugo theme